In the opening Star Wars-style crawl text sequence, to the bottom right of the pocket protector, you can see a black strip that obscures the stars in the background, revealing that the pocket protector is really just being "dragged along."
The nerds fall into a pit on the island where military supplies are hidden - which is an underground cave. In the scenes that follow, they are in a ground-level shack with open windows and daylight pouring through, not an underground cave.
When the Trilambs have been forced to strip to their underwear by the Alpha Beta's, Lewis is seen wearing a pair of white Y-Front briefs, yet when they arrive back at the Hotel Coral Essex after hitchhiking for five hours, he is now wearing longer and less revealing shorts, with no explanation for the change.
In the first movie, Wormser is seen to be about 11 years old. In this movie he looks to be about 15. It's been established that this movie takes place one year after the events of the first one so Wormser should be 12.
At 6 Minutes 32 Seconds Ogre is looking through a pair of binoculars and says "They're Here" (Like In POLTERGEIST) as the TriLams arrive at the airport to fly to Florida. Shouldnt he have delivered that line after they landed in Florida?
The nerds are discussing the average temperature as a function of lat/long, and they mention a position that has a East-West latitude and a North-South longitude. These are reversed - actually latitude is N/S and longitude is E/W.
When the Nerds are on their way to the airport from Adams College (which is supposed to be University of Arizona) they pass a sign that says "Old Floridian" in the background (the scene was shot in Fort Lauderdale).
In the scene where the Alpha Betas are in the hotel suite previously occupied by the Tri-Lambs before their arrest when framed for grand theft auto, Stewart shows up in a White Castle uniform looking for his "homies." There are no White Castle restaurants in Florida.
During the jail scene, two of the boys are playing chess. Considering they are experienced players (Skolnick's remark at the beginning of the movie); they should have seen that the board was in the wrong position.
The nerds are being forced to remove their clothes and chant after witnessing the sacrifice of the virgin at the Seminole Fortress/Alligator Pit. As they are running out of the pit, Lamar tries to grab his shirt and drops it. As he drops it, the shirt falls into the Alligator pit. The actor playing a Seminole Warrior attempts to catch it with his foot before it falls into the pit.
When Roger first meets Lewis, he introduces Buzz as the hotel manager. Yet when Lewis confronts Buzz following Stewart's being fired, he asks Buzz "are you the manager?" as if he had never seen him before.